forked from lijiext/lammps
226 lines
8.6 KiB
Plaintext
226 lines
8.6 KiB
Plaintext
LAMMPS (20 Mar 2014-ICMS)
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WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
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using 1 OpenMP thread(s) per MPI task
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# Solvated 5-mer peptide
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units real
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atom_style full
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pair_style lj/charmm/coul/long 8.0 10.0 10.0
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bond_style harmonic
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angle_style charmm
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dihedral_style charmm
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improper_style harmonic
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kspace_style pppm 0.0001
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read_data data.peptide
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orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
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1 by 1 by 2 MPI processor grid
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reading atoms ...
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2004 atoms
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reading velocities ...
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2004 velocities
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scanning bonds ...
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3 = max bonds/atom
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scanning angles ...
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6 = max angles/atom
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scanning dihedrals ...
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14 = max dihedrals/atom
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scanning impropers ...
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1 = max impropers/atom
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reading bonds ...
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1365 bonds
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reading angles ...
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786 angles
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reading dihedrals ...
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207 dihedrals
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reading impropers ...
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12 impropers
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4 = max # of 1-2 neighbors
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7 = max # of 1-3 neighbors
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14 = max # of 1-4 neighbors
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18 = max # of special neighbors
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neighbor 2.0 bin
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neigh_modify delay 5
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timestep 2.0
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group peptide type <= 12
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84 atoms in group peptide
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group one id 2 4 5 6
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4 atoms in group one
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group two id 80 82 83 84
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4 atoms in group two
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group ref id 37
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1 atoms in group ref
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group colvar union one two ref
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9 atoms in group colvar
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fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
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shell "rm -f peptide2.colvars.*"
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fix 2 all colvars peptide.colvars2 output peptide2
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fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
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19 = # of size 2 clusters
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6 = # of size 3 clusters
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3 = # of size 4 clusters
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640 = # of frozen angles
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#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
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#dump_modify 1 sort id
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thermo_style custom step temp etotal pe ke epair ebond f_2
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thermo 10
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run 100
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PPPM initialization ...
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G vector (1/distance) = 0.268725
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grid = 15 15 15
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0228209
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estimated relative force accuracy = 6.87243e-05
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using double precision FFTs
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3d grid and FFT values/proc = 6776 1800
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colvars: Creating proxy instance
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colvars: ----------------------------------------------------------------------
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colvars: Initializing the collective variables module, version 2013-10-22.
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colvars: # indexFile = "" [default]
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colvars: # analysis = off [default]
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colvars: # colvarsTrajFrequency = 1
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colvars: # colvarsRestartFrequency = 1000
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colvars: # colvarsTrajAppend = off [default]
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colvars: The restart output state file will be "rest.colvars.state".
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colvars: The final output state file will be "peptide2.colvars.state".
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colvars: Writing to colvar trajectory file "peptide2.colvars.traj".
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colvars: ----------------------------------------------------------------------
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colvars: Initializing a new collective variable.
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colvars: # name = one
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colvars: Initializing a new "distance" component.
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colvars: # componentCoeff = 1 [default]
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colvars: # componentExp = 1 [default]
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colvars: # period = 0 [default]
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colvars: # wrapAround = 0 [default]
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colvars: # forceNoPBC = off [default]
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colvars: # oneSiteSystemForce = off [default]
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colvars: Initializing atom group "group1".
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colvars: # indexGroup = "" [default]
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colvars: # psfSegID = [default]
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colvars: # atomsFile = "" [default]
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colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
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colvars: # enableForces = on [default]
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colvars: # disableForces = off [default]
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colvars: # centerReference = off [default]
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colvars: # rotateReference = off [default]
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colvars: # enableFitGradients = on [default]
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colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 0.
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colvars: Initializing atom group "group2".
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colvars: # indexGroup = "" [default]
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colvars: # psfSegID = [default]
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colvars: # atomsFile = "" [default]
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colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
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colvars: # enableForces = on [default]
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colvars: # disableForces = off [default]
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colvars: # centerReference = off [default]
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colvars: # rotateReference = off [default]
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colvars: # enableFitGradients = on [default]
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colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 0.
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colvars: All components initialized.
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colvars: # width = 1 [default]
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colvars: # lowerBoundary = 0 [default]
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colvars: # lowerWallConstant = 0 [default]
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colvars: # upperBoundary = 0 [default]
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colvars: # upperWallConstant = 0 [default]
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colvars: # expandBoundaries = off [default]
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colvars: # extendedLagrangian = off [default]
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colvars: # outputValue = on [default]
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colvars: # outputVelocity = off [default]
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colvars: # outputSystemForce = off [default]
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colvars: # outputAppliedForce = off [default]
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colvars: ----------------------------------------------------------------------
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colvars: Collective variables initialized, 1 in total.
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colvars: ----------------------------------------------------------------------
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colvars: Initializing a new "harmonic" instance.
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colvars: # name = h_pot
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colvars: # colvars = { one }
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colvars: # outputEnergy = off [default]
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colvars: # forceConstant = 100
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colvars: # centers = { 10 }
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colvars: # targetCenters = { 10 } [default]
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colvars: # targetForceConstant = 0 [default]
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colvars: # outputCenters = off [default]
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colvars: # outputAccumulatedWork = off [default]
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colvars: ----------------------------------------------------------------------
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colvars: Collective variables biases initialized, 1 in total.
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colvars: ----------------------------------------------------------------------
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colvars: Collective variables module initialized.
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colvars: ----------------------------------------------------------------------
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colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
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colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 15.035.
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SHAKE stats (type/ave/delta) on step 0
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4 1.111 1.44264e-05
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6 0.996998 7.26967e-06
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8 1.08 1.32536e-05
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10 1.111 1.22749e-05
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12 1.08 1.11767e-05
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14 0.96 0
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18 0.957206 4.37979e-05
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31 104.519 0.00396029
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Memory usage per processor = 10.4103 Mbytes
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Step Temp TotEng PotEng KinEng E_pair E_bond 2
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0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
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10 333.47973 -4982.3893 -6324.0116 1341.6223 -6400.417 21.367753 12.393269
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20 309.56974 -4999.4934 -6244.9234 1245.43 -6401.6969 43.595447 13.004393
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30 316.97689 -5025.5598 -6300.7895 1275.2297 -6422.5335 27.323113 6.7588862
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40 297.55811 -5088.2155 -6285.3215 1197.106 -6395.3714 13.676871 25.625154
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50 296.80002 -5117.2927 -6311.3488 1194.0561 -6451.8274 30.631277 5.3320302
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60 281.72798 -5188.494 -6321.9138 1133.4198 -6427.8833 26.28765 20.573958
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70 277.26045 -5224.8416 -6340.2881 1115.4465 -6447.8495 27.742889 0.69414895
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80 268.01458 -5281.8501 -6360.0996 1078.2495 -6496.6062 20.300729 5.260642
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90 270.43384 -5334.0847 -6422.0671 1087.9824 -6563.2486 39.845992 1.183249
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SHAKE stats (type/ave/delta) on step 100
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4 1.11096 0.000191466
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6 0.996989 3.5552e-05
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8 1.08 9.10001e-06
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10 1.111 1.58547e-05
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12 1.08 5.80613e-06
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14 0.959997 0
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18 0.957198 2.92454e-05
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31 104.52 0.00239929
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100 260.35617 -5387.2298 -6434.6687 1047.4389 -6534.1957 20.246734 0.075048991
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Loop time of 1.07439 on 2 procs for 100 steps with 2004 atoms
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98.2% CPU use with 2 MPI tasks x 1 OpenMP threads
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Performance: 16.084 ns/day 1.492 hours/ns 93.076 timesteps/s
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MPI task timings breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.77154 | 0.77308 | 0.77462 | 0.2 | 71.96
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Bond | 0.0023637 | 0.0025266 | 0.0026896 | 0.3 | 0.24
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Kspace | 0.095779 | 0.097411 | 0.099043 | 0.5 | 9.07
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Neigh | 0.15521 | 0.15521 | 0.15522 | 0.0 | 14.45
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Comm | 0.018134 | 0.018364 | 0.018594 | 0.2 | 1.71
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Output | 0.00024295 | 0.00032854 | 0.00041413 | 0.5 | 0.03
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Modify | 0.024936 | 0.024973 | 0.02501 | 0.0 | 2.32
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Other | | 0.002498 | | | 0.23
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Nlocal: 1002 ave 1010 max 994 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 8645 ave 8652 max 8638 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 354116 ave 356373 max 351860 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 708233
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Ave neighs/atom = 353.41
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Ave special neighs/atom = 2.34032
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Neighbor list builds = 13
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Dangerous builds = 1
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colvars: Saving collective variables state to "peptide2.colvars.state".
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Please see the log.cite file for references relevant to this simulation
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